top of page
Asian Institute of Research, Journal Publication, Journal Academics, Education Journal, Asian Institute
Asian Institute of Research, Journal Publication, Journal Academics, Education Journal, Asian Institute

Journal of Health and Medical Sciences

ISSN 2622-7258

Screen Shot 2018-08-12 at 1.24.09 AM.png
Screen Shot 2018-08-12 at 1.24.02 AM.png
Screen Shot 2018-08-12 at 1.23.57 AM.png
Screen Shot 2018-08-12 at 1.23.52 AM.png
open access

Published: 22 June 2023

Comparison of the Effectiveness in Nasopharyngeal, Throat, Saliva, and Nasal Swab Sample Media of Detection SARS-Cov-2 using RT-PCR

Raka Rajendra, Syahrul Tuba, Syed Azhar Syed Sulaiman

Indonesia Defense University (Indonesia), University Sains Malaysia (Malaysia)

journal of social and political sciences
pdf download

Download Full-Text Pdf



Pages: 72-78

Keywords: SARS-CoV-2, RT-PCR, Covid-19


To evaluate effectivity results among Nasopharyngeal, Throat, Saliva, and Nasal Swab Sample Media for Detection of SARS-Cov-2 virus using RT-PCR. SARS-CoV-2 is a coronavirus microorganism found in humans. A known viral infection causes the covid-19 disease to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Covid-19 has confused the public because of the different places where the samples were taken. Sampling was taken from the Nasopharynx, Throat, Saliva, and nasal Swab. This study used mini-review journals from several leading search engine journals such as PubMed, Elsevier, Jama Network, BMJ, Cochrane, Wiley, medRXiv, Lancet, and others, as well as from government websites such as WHO selected between 2020 and 2021 in the English language. Each sampling place has its advantages and disadvantages. Any place that is used as the gold standard is the nasal swab and nasopharyngeal. This paper attempts to compare the efficacy of four sample media to find the best method for detecting the SARS-CoV-2 virus. It is hoped that repeating this paper can make us aware of every method that we can use to detect the SARS-CoV-2 virus and reduce the spread of this virus, which is increasingly widespread.


  1. Afzal, A.  (2020). Molecular diagnostic technologies for COVID-19: Limitations and  challenges. In Journal of Advanced Research (Vol. 26, p. 149‑159).  Elsevier B.V.

  2. Astuti, I.,  & Ysrafil. (2020). Severe Acute Respiratory Syndrome Coronavirus 2  (SARS-CoV-2): An overview of viral structure and host response. Diabetes  and Metabolic Syndrome: Clinical Research and Reviews, 14(4), 407‑412.

  3. Berenger,  B. M., Fonseca, K., Schneider, A. R., Hu, J., & Zelyas, N. (2020).  Sensitivity of nasopharyngeal, nasal and throat swab for the detection of  SARS-CoV-2. In medRxiv. medRxiv.

  4. Chan, J. F.  W., Yuan, S., Kok, K. H., To, K. K. W., Chu, H., Yang, J., Xing, F., Liu, J.,  Yip, C. C. Y., Poon, R. W. S., Tsoi, H. W., Lo, S. K. F., Chan, K. H., Poon,  V. K. M., Chan, W. M., Ip, J. D., Cai, J. P., Cheng, V. C. C., Chen, H., …  Yuen, K. Y. (2020). A familial cluster of pneumonia associated with the 2019  novel coronavirus indicating person-to-person transmission: a study of a  family cluster. The Lancet, 395(10223), 514‑523.

  5. Deepak, S.  A., Kottapalli, K. R., Rakwal, R., Oros, G., Rangappa, K. S., Iwahashi, H.,  Masuo, Y., & Agrawal, G. K. (2007). Real-Time PCR: Revolutionizing  Detection and Expression Analysis of Genes. In Current Genomics (Vol.  8).

  6. Dogan, O.  A., Kose, B., Agaoglu, N. B., Yildiz, J., Alkurt, G., Demirkol, Y. K., Irvem,  A., Doganay, G. D., & Doğanay, L. (2020). Does sampling saliva increase  detection of SARS-CoV-2 by RT-PCR? Comparing saliva with oro-nasopharyngeal  swabs. In medRxiv. medRxiv.

  7. la Marca,  A., Capuzzo, M., Paglia, T., Roli, L., Trenti, T., & Nelson, S. M. (2020).  Testing for SARS-CoV-2 (COVID-19): a systematic review and clinical guide to  molecular and serological in-vitro diagnostic assays. In Reproductive  BioMedicine Online (Vol. 41, Numéro 3, p. 483‑499). Elsevier Ltd.

  8. Matheson,  N. J., & Lehner, P. J. (2020). How does SARS-CoV-2 cause COVID-19? Science,  369(6503), 510.

  9. Medeiros da  Silva, R. C., Nogueira Marinho, L. C., de Araújo Silva, D. N., Costa de Lima,  K., Pirih, F. Q., & Luz de Aquino Martins, A. R. (2020). Saliva as a  possible tool for the SARS-CoV-2 detection: A review. In Travel Medicine  and Infectious Disease (Vol. 38). Elsevier Inc.

  10. Nasiri, K.,  & Dimitrova, A. (2021). Comparing saliva and nasopharyngeal swab specimens  in the detection of COVID-19: A systematic review and meta-analysis. In Journal  of Dental Sciences. Association for Dental Sciences of the Republic of  China.

  11. Péré, H.,  Péré, H., Péré, H., Podglajen, I., Podglajen, I., Wack, M., Wack, M.,  Flamarion, E., Mirault, T., Mirault, T., Goudot, G., Goudot, G.,  Hauw-Berlemont, C., Le, L., Le, L., Caudron, E., Caudron, E., Carrabin, S.,  Rodary, J., … Veyer, D. (2020). Nasal swab sampling for SARS-CoV-2: A  convenient alternative in times of nasopharyngeal swab shortage. In Journal  of Clinical Microbiology (Vol. 58, Numéro 6). American Society for  Microbiology.

  12. Perera, R.  A. P. M., Tso, E., Tsang, O. T. Y., Tsang, D. N. C., Fung, K., Leung, Y. W.  Y., Chin, A. W. H., Chu, D. K. W., Cheng, S. M. S., Poon, L. L. M., Chuang, V.  W. M., & Peiris, M. (2020). SARS-CoV-2 virus culture and subgenomic RNA  for respiratory specimens from patients with mild Coronavirus disease. Emerging  Infectious Diseases, 26(11), 2701‑2704.

  13. Pondaven-Letourmy,  S., Alvin, F., Boumghit, Y., & Simon, F. (2020). How to perform a  nasopharyngeal swab in adults and children in the COVID-19 era. European  Annals of Otorhinolaryngology, Head and Neck Diseases, 137(4), 325‑327.

  14. Rabaan, A. A.,  Tirupathi, R., Sule, A. A., Aldali, J., Mutair, A. al, Alhumaid, S., Muzaheed,  Gupta, N., Koritala, T., Adhikari, R., Bilal, M., Dhawan, M., Tiwari, R.,  Mitra, S., Emran, T. bin, & Dhama, K. (2021). Viral Dynamics and Real-Time  RT-PCR Ct Values Correlation with Disease Severity in COVID-19. Diagnostics,  11(6), 1091.

  15. Ranoa, D.  R. E., Holland, R. L., Alnaji, F. G., Green, K. J., Wang, L., Brooke, C. B.,  Burke, M. D., Fan, T. M., & Hergenrother, P. J. (2020). Saliva-based  molecular testing for SARS-CoV-2 that bypasses RNA extraction. In bioRxiv.  bioRxiv.

  16. To, K.  K.-W., Tsang, O. T.-Y., Yip, C. C.-Y., Chan, K.-H., Wu, T.-C., Chan, J. M.-C.,  Leung, W.-S., Chik, T. S.-H., Choi, C. Y.-C., Kandamby, D. H., Lung, D. C.,  Tam, A. R., Poon, R. W.-S., Fung, A. Y.-F., Hung, I. F.-N., Cheng, V. C.-C.,  Chan, J. F.-W., & Yuen, K.-Y. (2020). Consistent Detection of 2019 Novel  Coronavirus in Saliva. Clinical Infectious Diseases : An Official  Publication of the Infectious Diseases Society of America, 71(15),  841‑843.

  17. Torres, I.,  Albert, E., & Navarro, D. (2020). Pooling of nasopharyngeal swab specimens  for SARS-CoV-2 detection by RT-PCR. In medRxiv. medRxiv.

  18. Tsujimoto,  Y., Terada, J., Kimura, M., Moriya, A., Motohashi, A., Izumi, S., Kawajiri,  K., Hakkaku, K., Morishita, M., Saito, S., Takumida, H., Watanabe, H.,  Tsukada, A., Morita, C., Yamaguchi, Y., Katsuno, T., Kusaba, Y., Sakamoto, K.,  Hashimoto, M., … Sugiyama, H. (2021). Diagnostic accuracy of nasopharyngeal  swab, nasal swab and saliva swab samples for the detection of SARS-CoV-2 using  RT-PCR. Infectious Diseases.

  19. van Kampen,  J. J. A., van de Vijver, D. A. M. C., Fraaij, P. L. A., Haagmans, B. L.,  Lamers, M. M., Okba, N., van den Akker, J. P. C., Endeman, H., Gommers, D. A.  M. P. J., Cornelissen, J. J., Hoek, R. A. S., van der Eerden, M. M.,  Hesselink, D. A., Metselaar, H. J., Verbon, A., de Steenwinkel, J. E. M.,  Aron, G. I., van Gorp, E. C. M., van Boheemen, S., … van der Eijk, A. A.  (2020). Shedding of infectious virus in hospitalized patients with coronavirus  disease-2019 (COVID-19): duration and key determinants. medRxiv,  2020.06.08.20125310.

  20. Wikramaratna,  P. S., Paton, R. S., Ghafari, M., & Lourenço, J. (2020). Estimating the  false-negative test probability of SARS-CoV-2 by RT-PCR. In medRxiv.  medRxiv.

  21. Xiao, A.  T., Tong, Y. X., Gao, C., Zhu, L., Zhang, Y. J., & Zhang, S. (2020).  Dynamic profile of RT-PCR findings from 301 COVID-19 patients in Wuhan, China:  A descriptive study. Journal of Clinical Virology, 127.

  22. Yamayoshi,  S., Sakai-Tagawa, Y., Koga, M., Akasaka, O., Nakachi, I., Koh, H., Maeda, K.,  Adachi, E., Saito, M., Nagai, H., Ikeuchi, K., Ogura, T., Baba, R., Fujita,  K., Fukui, T., Ito, F., Hattori, S. I., Yamamoto, K., Nakamoto, T., … Kawaoka,  Y. (2020). Comparison of Rapid Antigen Tests for COVID-19. Viruses, 12(12).

  23. Young, B.  E., Ong, S. W. X., Ng, L. F. P., Anderson, D. E., Chia, W. N., Chia, P. Y.,  Ang, L. W., Mak, T.-M., Kalimuddin, S., Chai, L. Y. A., Pada, S., Tan, S. Y.,  Sun, L., Parthasarathy, P., Fong, S.-W., Chan, Y.-H., Tan, C. W., Lee, B.,  Rötzschke, O., … Team, S. 2019 N. C. O. R. (2020). Viral Dynamics and Immune  Correlates of Coronavirus Disease 2019 (COVID-19) Severity. Clinical  Infectious Diseases.

  24. Zou, L.,  Ruan, F., Huang, M., Liang, L., Huang, H., Hong, Z., Yu, J., Kang, M., Song,  Y., Xia, J., Guo, Q., Song, T., He, J., Yen, H.-L., Peiris, M., & Wu, J.  (2020). SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected  Patients. The New England Journal of Medicine, 382(12), 1177‑1179.

bottom of page